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  • PANGAEA  (7)
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  • 1
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    Transcriptomic and histological analysis (Light and Transmission Electron Microscopy) on five Geodia species to identify their reproductive status and the gene expression during gametogenesis (2020)
    PANGAEA
    In:  Natural History Museum
    Details
    Publication Date: 2023-03-03
    Description: The collected samples of Geodia species were used to identify if they were reproductive and understand which genes are expressed during gametogenesis. Specifically, specimens fixed in glutaraldehyde solution, were processed for histological analysis to observe gametes in the sponge tissue. Once, we identified male, female (while in gametogenesis) and non-reproductive specimens, we used the RNAlater fixed samples to extract RNA from those specimens. Then, we prepared cDNA libraries, sequenced them with illumina nextseq and we did differential gene expression analysis in order to compare the expressed genes in male vs female specimens and vs non-reproductive specimens. The goal was to understand the molecular machinery of gametogenesis in sponges from an evolutionary point of view.
    Keywords: Agassiz Trawl; AGT; Area/locality; DATE/TIME; Deep-sea Sponge Grounds Ecosystems of the North Atlantic; Depth, bathymetric; Device type; Dredge, triangle; Event label; G. O. Sars (2003); gametogenesis; Geodia sp.; GS16A-202; GS2016109A; GS2016109A-06-ROV-01; GS2017110; GS2017110-09-ROV-6; GS2017110-23-ROV12; GS2017110-57-AGT-01; Hans Brattström; HB2016944; HB2016944_2; HB2016952; HB2016952_6; Investigator; Korsfjord; Kosterfjord; Latitude of event; Longitude of event; Nereus; Nereus20160405; Nereus20160405_ROV; Porifera; Remote operated vehicle; ROV; Sample code/label; Schultz Bank; Sex; Species; SponGES; Sula reef; TAD; Transcriptomics; Tromsøflaket
    Type: Dataset
    Format: text/tab-separated-values, 245 data points
    Location Call Number Expected Availability
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    DATA PANGAEA
  • 2
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    Microsatellite genotyping of Mediterranean population of Ircinia fasciculata and Ircinia variabilis (2016)
    PANGAEA
    In:  Supplement to: Riesgo, Ana; Pérez-Portela, Rocío; Pita, Lucía; Blasco, Gema; Erwin, Patrick S; López-Legentil, Susanna (2016): Population structure and connectivity in the Mediterranean sponge Ircinia fasciculata are affected by mass mortalities and hybridization. Heredity, https://doi.org/10.1038/hdy.2016.41
    Details
    Publication Date: 2023-03-08
    Description: Recent episodes of mass mortalities in the Mediterranean Sea have been reported for the closely related marine sponges Ircinia fasciculata and I. variabilis, which live in sympatry. In this context, the assessment of the genetic diversity, bottlenecks and connectivity of these sponges has become urgent in order to evaluate the potential effects of mass mortalities on their latitudinal range. Our study aims to establish 1.) the genetic structure, connectivity, and signs of bottlenecks across the populations of I. fasciculata, and 2.) the hybridization levels between I. fasciculata and I. variabilis. To accomplish the first objective, 194 individuals of I. fasciculata from 12 locations across the Mediterranean were genotyped at 14 microsatellite loci. For the second objective, mitochondrial cytochrome c oxidase subunit I sequences of 16 individuals from both species were analyzed along with genotypes at 12 microsatellite loci of 40 individuals coexisting in 3 Mediterranean populations. We detected strong genetic structure along the Mediterranean for I. fasciculata, with high levels of inbreeding in all locations and bottleneck signs in most locations. Oceanographic barriers like the Almeria-Oran front, North-Balearic front, and the Ligurian-Thyrrenian barrier seem to be impeding gene flow for I. fasciculata, adding population divergence to the pattern of isolation by distance derived from the low dispersal abilities of sponge larvae. Hybridization between both species occurred in some populations, which might be increasing genetic diversity and somewhat palliating the genetic loss caused by population decimation in I. fasciculata
    Keywords: File content; File name; File size; Mediterranean_Sea; Mediterranean Sea; Uniform resource locator/link to file
    Type: Dataset
    Format: text/tab-separated-values, 8 data points
    Location Call Number Expected Availability
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    DATA PANGAEA
  • 3
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    Metadata, flow cytometry data, and NCBI-Accession numbers (16S, 18S, COI, and SNP data) for fan-shaped sponges and seawater from the Cantabrian Sea in summer 2017 (2020)
    PANGAEA
    Details
    Publication Date: 2023-03-25
    Description: Connectivity is a fundamental process driving the persistence of marine populations and their adaptation potential in response to environmental change. In this study, we analysed the population genetics of two morphologically highly similar deep-sea sponge clades (Phakellia hirondellei and the 'Topsentia-and-Petromica (TaP)' clade) at three locations in the Cantabrian Sea. Sponge taxonomy was assessed by spicule analyses, as well as by 18S sequencing and COI sequencing. The corresponding host microbiome was analysed by 16S rRNA gene sequencing. In addition we set up an oceanographic modelling framework, for which we used seawater flow cytometry data (derived from bottom depths of CTD casts) as ground-truthing data.
    Keywords: Accession number, genetics; amplicon sequencing; Angeles Alvarino; Area/locality; Bacteria; Bay of Biscay; CTD/Rosette; CTD1; CTD10; CTD11; CTD12; CTD13; CTD14; CTD15; CTD2; CTD3; CTD4; CTD5; CTD6; CTD7; CTD8; CTD9; CTD-RO; Date/Time of event; Deep-sea Sponge Grounds Ecosystems of the North Atlantic; DEPTH, water; DR10; DR15; DR4; DR7; DR9; Dredge, rock; DRG_R; Event label; flow cytometry; Flow cytometry; Geology, comment; Latitude of event; Longitude of event; Measurement conducted; Method/Device of event; Phytoplankton; population genetics; Porifera; Sample code/label; Sample ID; single-nucleotide polymorphisms (SNPs); SponGES; SponGES_0617; SPONGES_0617_04-DR4; SPONGES_0617_07-CTD1; SPONGES_0617_12-CTD2; SPONGES_0617_13-CTD3; SPONGES_0617_15-DR7; SPONGES_0617_18-CTD4; SPONGES_0617_19-CTD5; SPONGES_0617_23-DR9; SPONGES_0617_24-CTD6; SPONGES_0617_27-CTD7; SPONGES_0617_28-DR10; SPONGES_0617_29-CTD8; SPONGES_0617_40-CTD9; SPONGES_0617_42-CTD10; SPONGES_0617_46-CTD11; SPONGES_0617_49-CTD12; SPONGES_0617_55-CTD13; SPONGES_0617_58-CTD14; SPONGES_0617_60-DR15; SPONGES_0617_61-CTD15
    Type: Dataset
    Format: text/tab-separated-values, 550 data points
    Location Call Number Expected Availability
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    DATA PANGAEA
  • 4
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    Allele matrix of 10 microsatellites in Petrosia ficiformis (2017)
    PANGAEA
    In:  Supplement to: Riesgo, Ana; Taboada, Sergi; Pérez-Portela, Rocío; Melis, Paolo; Xavier, Joana R; Blasco, Gema; López-Legentil, Susanna (2019): Genetic diversity, connectivity and gene flow along the distribution of the emblematic Atlanto-Mediterranean sponge Petrosia ficiformis (Haplosclerida, Demospongiae). BMC Evolutionary Biology, 19(1), https://doi.org/10.1186/s12862-018-1343-6
    Details
    Publication Date: 2023-01-13
    Description: The allele matrix contains the genotypes (coded as length of fragments) for 10 microsatellite markers described in Taboada et al. (2015). There are 280 individuals for 10 populations across the Atlanto-Mediterranean distribution of the species.
    Keywords: Blanes; MULT; Multiple investigations
    Type: Dataset
    Format: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, 192.5 kBytes
    Location Call Number Expected Availability
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    DATA PANGAEA
  • 5
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    Collection information of the genus Geodia from boreo-arctic North-Atlantic deep-sea sponge grounds (2020)
    PANGAEA
    In:  Natural History Museum
    Details
    Publication Date: 2023-03-03
    Description: Boreo-arctic sponge grounds are essential deep-sea structural habitats that provide important services for the ecosystem. These large sponge aggregations are dominated by demosponges of the genus Geodia (order Tetractinellida, family Geodiidae). However, little is known about the basic biological features of these species, such as their life cycle and dispersal capabilities. Here, we surveyed five deep-sea species of Geodia from the North Atlantic Ocean and studied their reproductive cycle and strategy using light and electron microscopy. We confirmed that these five species were oviparous and gonochoristic and that their reproductive season spanned similar periods: from late spring to early autumn. Concerning their reproductive strategy, the high abundance of lipid yolk observed in the female gametes could indicate both a necessity for rapid fuel during embryogenesis in the water column and increased buoyancy for drifting over longer times. Overall, the investment in reproduction was lower for all the surveyed species compared to similar shallow-water species. Given the present hazards that threaten sponge grounds, it becomes crucial to understand the processes behind the maintenance and regeneration of populations of keystone deep-sea species in order to predict the magnitude of human impacts and estimate their ability to recover. The information provided in this study will be useful for developing adequate conservation strategies for these vulnerable deep-sea habitats.
    Keywords: Agassiz Trawl; AGT; Area/locality; Campaign; DATE/TIME; Deep-sea Sponge Grounds Ecosystems of the North Atlantic; DEPTH, water; Device type; Dredge, triangle; Event label; G. O. Sars (2003); Geodia; GS16A-202; GS2016109A; GS2016109A-06-ROV-01; GS2017110; GS2017110-09-ROV-6; GS2017110-23-ROV12; GS2017110-41-ROV-19; GS2017110-57-AGT-01; GS2017110-68-ROV-25; GS2017110-74-ROV-26; Hans Brattström; HB2016944; HB2016944_2; HB2016952; HB2016952_6; Histology; Investigator; KB2017610; KB2017610_DRG_43; Korsfjord; Kosterfjord; Kosterfjord_March_2019; Kristine Bonnevie; Latitude of event; Longitude of event; Nereus; Nereus20160405; Nereus20160405_ROV; Nsvalbard_2011-09-22; Porifera; Remote operated vehicle; Reproduction; Rosemary_Bank_2011-09-11; Rosemary_Bank_2012-09-19; Rosemary_Bank_2015-09-20; Rosemary_Bank_2016-09-19; Rosemary_Bank_2016-09-20; Rosemary Bank; ROV; Sample ID; Schultz Bank; Sex; Species; SponGES; Sula reef; Svalbard; TAD; Tromsøflaket
    Type: Dataset
    Format: text/tab-separated-values, 810 data points
    Location Call Number Expected Availability
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    DATA PANGAEA
  • 6
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    Allele matrix of 11 microsatellites in Plenaster craigi for 4 areas and 30 populations (2018)
    PANGAEA
    In:  Supplement to: Taboada, Sergi; Riesgo, Ana; Wiklund, Helena; Paterson, Gordon L J; Koutsouveli, Vasiliki; Santodomingo, Nadia; Dale, Andrew C; Smith, Craig R; Jones, Daniel O B; Dahlgren, Thomas G; Glover, Adrian G (2018): Implications of population connectivity studies for the design of marine protected areas in the deep sea: An example of a demosponge from the Clarion-Clipperton Zone. Molecular Ecology, 27(23), 4657-4679, https://doi.org/10.1111/mec.14888
    Details
    Publication Date: 2024-05-18
    Description: The excel file has two spread-sheets: (i) "Microsatellites-4Areas" including the information of the 11 microsatellites used in the paper for the four different areas we investigated; (ii) "Microsatellites-30Populations" including the information of the 11 microsatellites used in the paper for the 30 different populations we investigated. In the two spread-sheets we include the following columns: "Number of individual" from 1 to 168; "Area" with the names of the areas or populations for every individual; "Sample Code" with the name of the sample used in the paper; "1Ple, 3Ple, 11Ple, 13Ple, 12Ple, 14Ple, 16Ple, 5Ple, 19Ple, 10Ple, and 2Ple" the name of each of the 11 microsatellites gentotyped in our study. In addition to that, we provide a small summary of the "Number of microsatellites", "Number of Individuals", "Number of Areas", "Number of Populations", and "N of individuals per area and population".
    Type: Dataset
    Format: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, 89.7 kBytes
    Location Call Number Expected Availability
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    DATA PANGAEA
  • 7
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    Microsatellite genotyping of Mediterranean population (2016)
    PANGAEA
    In:  EPIC3Bremerhaven, PANGAEA
    Details
    Publication Date: 2016-04-27
    Repository Name: EPIC Alfred Wegener Institut
    Type: PANGAEA Documentation , notRev
    Format: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
    Format: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
    Location Call Number Expected Availability
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    PAPER (OA)
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